Stargate Atlantis (Season 1: rewritten)
by CSIRide-Kirk
Summary: Major Jessica Sheppard didn't expect to be introduced to a life of craziness when she flew Jack O'Neill to Antarctica. Yet, she was placed in charge of the military garrison on the Atlantis expedition and was introduced to the Wraiths, the enemy of Atlantis. She and her team (AR-1) swear to defend their city and home to their dying breaths. Follows the show. Fem!John Sheppard.


**Episode 1: Rising**

When the ancient people of Atlantis left their city under the water on earth to escape a plague that was destroying them, only one remained behind to preserve their culture.

* * *

 _Ten thousand years later_

Major Jessica Sheppard was flying a helicopter to Antarctica with Brigadier General Jack O'Neill when an out of control drone nearly killed them before it stopped. Jessica looked at Jack and muttered "that was different" Jack just said "me? Not so much." Jessica got the helicopter back in the air and soon landed at the base she was heading towards. Meanwhile in the base, a sergeant reported what Jessica said to Daniel, Rodney, Elizabeth and Carson "seven minutes out" he acknowledged "thank god" Elizabeth sighed, glancing at Rodney before looking at a pale Carson in the control chair "oh holy crap" the Scotsman muttered.

"Jack!" Daniel Jackson exclaimed as his old commanding officer came down with a black haired girl who was wide eyed "Daniel, warm welcome" Jack said sarcastically "wasn't me, how did you..?" "Stop my ass getting blown outta the sky? The exceptional flying of one Major Jessica Sheppard, she likes it here" Jack answered his question. Daniel looked at Jessica "exceptional? You like it here?" He said to her, Jessica just shrugged at Daniel.

Jack turned to Daniel and asked him why they needed him in Antarctica of all places, Daniel said he needed to speak with Dr Weir "hey, don't touch anything!" Jack snapped at Jessica, who shrugged again and went exploring the base, where she soon met Carson Beckett, the man who discovered the Ancient Technology Activation gene and had accidentally released the drone. Jessica accepted his apology and he began to explain the basics of the Stargate.

Daniel had been in an argument with Jack over the fact that he wanted to go on Elizabeth's expedition to find the ancient city of Atlantis, but Jack flatly refused him permission to go. He needed Daniel on earth and to keep an eye on the new members of SG-1.

Carson was showing Jessica the control chair and Jessica made to sit down "Major, please don't" he warned, Jessica waved him off "come on, what are the odds of me having the same gene?" She said. But the chair activated as she sat down "pretty slim, Dr Weir! don't move!" Carson said as he dashed off to get Elizabeth Weir. Elizabeth, Jack and Daniel rushed up with another man "who is this?" Elizabeth asked, looking at the confused Jessica Sheppard "I said don't touch anything" Jack said to her, she looked at him "Jack, I just sat down" she protested, the man beside Jack (Dr Rodney McKay) looked at her "Major, think about where we are in the solar system" he said to the still confused Major, yet Jessica pulled up the holograms with complete ease, Daniel, Jack, Rodney, Elizabeth and Carson looked confused on how she easily did it "did I do that?" she asked.

Jack had a discussion with Elizabeth about the expedition "no, I need Daniel here on earth" he told her, Elizabeth looked guiltily at him "I was talking about Major Sheppard" she said, Jack stopped at the elevator "don't you already have people who can use the ancient technology?" He asked. Elizabeth folded her arms "yes, but they need a significant amount of training and expertise. But Jessica Sheppard does it naturally" she said. "You know I'd check into her file" Jack said, Elizabeth nodded "I know about the black mark in Afghanistan, but she was trying to save the lives of three servicemen" she said, defending Jessica. Elizabeth knew she'd disobeyed her superior's direct orders.

"Disobeying a direct order in the process" Jack said, he was tired of Jessica's wild antics and disregard for the rules, Elizabeth had a trump card over Jack though "I have read your own file, General" she said, with a small smirk. Jack sighed "right, okay, it's your expedition. You want her? You ask her. Just watch her attitude, wild behaviour and short temper" he sais as he turned to leave on the elevator. Elizabeth looked at him "that's the thing sir, I already have" she admitted. Jack looked mildly surprised "really?"

* * *

Jessica sat at the controls of the helicopter, she had to ensure everything was working properly before she lifted off with Jack back to the base in Australia that they'd left before. Elizabeth's words were still echoing in her mind, she was wanted on a government program that was highly classified _and_ with her record? Never gonna ever happen. Jack came and climbed back into the helicopter as Jess sat back and fiddled with the locket that hung around her neck, it had been a birthday present from last year off her younger brother David. David was the only member of her family that loved her and respected her decision to join the Air Force, Patrick Sheppard had just beaten Jessica.

 _Seventeen Years ago:_

 _"Dad, I'm NOT following what you want! I wanna be a pilot!" Jessica had snapped, Patrick Sheppard had flown into a rage "you ungrateful selfish child!" He roared, grabbing his daughter by her arm "you aren't fit to be in the Air Force, you're deaf as a doorpost!" He snarled at her. Jessica whimpered in fear, pain and heartache at Patrick's words._

 _"You're the one who beat her so bad around the head that Jessie's hearing was permanently damaged!" David had snapped, Patrick had just slapped his younger son. David had been twelve and Jessica barely a year older than him. Patrick also always ignored the fact that Jessica was always unhappy on Christmas Eve as it was her birthday and he always ignored that fact. Vivian Sheppard had always made sure that Jessica and David remembered her birthday and always took Jessica out for a small meal or treat._

"Jess, Jess!" Jack brought her back to the present "huh? Sorry, Jack. I'm not sure if I should go" she said, Jack looked at her curiously "is it about your hearing difficulties?" He asked, Jessica shrugged "sorta, but I wouldn't be able to see my brother, David. He's the only member of my family that still speaks to me, remembers my birthday on December 24th other than just the fact it's Christmas eve and is proud of me in the Force. Then I'm nearly killed by an alien missile, I find out I've got a mutated alien gene, then about the Stargates, it's a little too much to handle at one time, Jack. I just dunno." she said, Jack sighed as Jessica pulled on her helmet and turned on the engines.

Jack was the only person in the air force to know about Jessica's disability. She'd told him the entire story of what had happened when she was a child, Jack had met her at a meeting in the Pentagon. Jessica had been uncomfortable in her Dress Blues and there was also Patrick Sheppard giving her glares and snapping awful things at his daughter, who now towered over him and was physically fit as he was overweight. David Sheppard had his arm around his sister and turned away from their father to calm Jessica.

Jack reached over and pulled his on "let me ask ya somethin', why did you wanna be a pilot?" He asked her, Jessica looked at him "just to fly like crazy" she mumbled, Jack looked at her "well, I'd say those who don't go through the Stargate are just as crazy" he sais, he told Jessica some of his adventures through the Gate. That sparked up Jessica's curiosity for the unknown "alright, maybe I'm too crazy, but yeah. I'll definitely go for some craziness" she said, giving Jack a wide and excitable grin. Jack smiled.

* * *

Elizabeth left her husband a video telling him about the Stargate program and information about the clearance he had to know about what she was going to do in Atlantis. The President had also given Jessica clearance to tell her brother about what she was going to get up to "just be careful, and Jess?" He said to her.

"What?"

"Don't die, please?"

"What am I? Seventeen?"

David laughed at his sister's sarcastic wit and attitude "don't piss off any aliens, I got it before you even ask" she said, David could tell she was getting irritated "don't kill anyone annoying on your team?" He asked. Jessica snorted "if Kavanagh watches his attitude about me, then I won't be sent back home to earth" Jessica said to her brother.

* * *

Jessica woke the next morning in her temporary quarters in the Cheyenne Mountain Complex, the headquarters of the Stargate Program, she pulled on her new (and also clean) Atlantis Reconnaissance Expedition uniform and hoisted her filled backpack onto her back before leaving the room to walk to the Stargate room. She passed several members of both the earthbound SG members and the Atlantis expedition when a Lieutenant shoved her out of the way and into Rodney McKay "outta my way, slut" he said.

Jessica was hurt, Rodney helped her back up and asked her if she was alright "yeah, who was that?" She asked "Aiden Ford, he's gonna need to watch his back with you, isn't he?" Rodney asked, telling the look on Jessica's face easily. Jessica nodded, storming off in the direction of the Gate room, Jack then walked up to Rodney "what happened?"

* * *

Jessica stood with the other members of the military for the expedition, Rodney was with Elizabeth after powering up the ZPM for the Stargate, the eight chevron fell into place on the symbol of earth, a pyramid with the sun on top for Cairo, Egypt where the Gate was discovered by Jack and Daniel with the original Stargate team, when the vortex expelled and created a stable wormhole. Rodney had by then went down to the room and was standing next to Jessica to keep her calm while next to Lieutenant Ford.

Elizabeth went through the Gate first with an armed escort, then Ford, Rodney and Jessica walked up to it "what's it like?" Jessica asked Rodney, Ford answered her mockingly "hurts like hell, Major" then ran through laughing at her fear. Rodney placed a hand on her shoulder "it's fine, it's like going on a waterslide at 600 m/ph" he said as the two went through. The room in Atlantis was dark when the others were through, until Jessica Sheppard arrived with Dr McKay, then everything in the room activated.

Jessica felt someone whisper in her mind " _Welcome to Atlantis, Major Sheppard_ " Jessica shuddered, Rodney looked at her "you okay?" He asked "yeah, just felt like someone just spoke in my head, but it wasn't me" she said, then heard a musical laughter "alright creepy" she thought. Then looked to find Elizabeth wanting her to follow her again.

The two looked out of the window with Rodney "oh my god, we're underwater" Elizabeth breathed "I'd say we're under several thousand feet of ocean" Jessica said, sarcastically. Elizabeth shot her a glare, Jessica shrugged "General O'Neill warned you" Rodney thought, with a mental laugh, at Jessica's wit and sarcasm at Elizabeth as well. "There's some sort of force field holding back the water" Rodney trailed off, then glanced back out the window "now that is impressive" Jessica laughed kindly at him.

* * *

Jessica still wondered what the voice in her mind was, she needed to know as it creped her out, as if the voice heard her it whispered in her mind again " _I am Atlantis, but no-one will know that I can speak to those I like_ " it said to her, Jessica thought back " _gal, thanks for telling me. I was kinda freaking out there_ " she heard the musical laugh and then it was silent. Then she heard Kavanagh "this place is a dump" " _Uh, Atlantis, you heard that right?_ " Jessica thought, she heard a giggle of childish laughter again.

After they got everyone through and the wormhole closed, not before Jack had sent through a bottle of champagne for them, Jessica volunteered to go on one of the first missions through the Atlantis gate, they met a small band of villagers of a race called Athosians, the woman they met wasnamed Teyla Emmagan. Teyla also saw that Jessica often fidgeted with something in her ears and asked her if they could talk privately in some caves that she knew of. Jessica didn't mind, she liked Teyla almost instantly.

Jessica told Teyla the reason why she fidgeted with the things in her ears "I'm stone deaf, I can't hear a thing without these" she said, showing Teyla her hearing aids. That made Teyla curious "do your leaders know of this?" She asked, Jessica shook her head "no, Elizabeth doesn't know and she's my commanding officer, but our doctor, Carson Beckett, knows. As does one of our generals back home on earth and a friend of mine back on Atlantis" Jessica explained to her and begged her never to tell anyone about it.

Teyla swore never to tell anyone, then Jessica noticed a necklace and picked it up. Giving it to Teyla as a gift between friends, then Jessica was summoned back to the village as an enemy named the Wraith had come through the gate and was attacking the village "move them to Atlantis!" She yelled, the Athosians followed the AR-1 team back through the gate while the scientists and Elizabeth were trying to keep the shield around Atlantis up. But the city moved itself to the surface when Jessica returned again.

* * *

Several marines had been caught by the Wraith and Jessica immediately took a PuddleJumper to go and get them, yet she was also stuck with Lieutenant Ford as well, who was now wary after seeing her lose her temper with Elizabeth earlier. The others found the captured marines and Athosians, but Jessica had taken off to another part of the ship to find their Colonel, she caught a Wraith feeding on him and shot him through the Wraith's hand to put him out of his misery. But Jessica was then stunned by a Wraith.

"Bring her to me" the queen hissed as an unconscious Jessica was thrown onto a table to wake her up "how's the hand feeling?" She said cockily, then asked the queen. The Queen looked at her right hand where Jessica had shot her, it had now healed "much better" she hissed, Jessica banged her head back on the table "I'm sorry to hear that" she said. Jessica knew that the Wraith didn't know about her deafness, but Atlantis had somehow changed her hearing aids so she could think them off and on, Jessica had them off so that she couldn't hear what the queen was saying afterwards. Then she saw the life signs detector in Jessica's bulletproof vest and snarled "how did this come to you?"

Luckily Jessica could lip-read "I don't remember" before having her head bashed against the table again. The Wraith Queen began to prepare for feeding on Jessica, but Lt Ford came and shot her off the Major. She still didn't like Ford, but she had to put up with him, she made it back to the 'Jumper and took off back to Atlantis chased by three Wraith Darts "we're going too fast!" Ford yelled, Jessica ignored him and went through the Stargate. The Darts hit the shield behind her and were destroyed.

* * *

The Athosians were welcomed in the city and Jessica had taken over as the military commander due to the death of Colonel Sumner. But there was something bothering the young Major, mainly with Lieutenant Ford. He suspected when Jessica ignored him that the Major was deaf, he'd secretly looked closer at her ears and saw a small nude coloured object in the top lobe. He needed to tell Elizabeth, but she would just deny it.

Teyla promised to help Jessica keep her secret, but even she suspected Ford knew and would try and oust the Major, get her kicked off Atlantis and thrown out of their Air Force. Many of the Generals suspected Jessica was deaf, but they didn't have any proof to say otherwise. The celebrations continued into the night and Jess assigned her soldiers their quarters. One disadvantage to jess was she was so abnormally tall, her feet dangled off the edge of her bed, but she was oddly enough comfortable with that.

* * *

 **Thus ends 'Rising'. I hope you lot enjoyed it. Stay tuned for the next episode of Stargate: Atlantis (Rewritten), continuing the story of the amazing city of the Ancients and the badass female version of John Sheppard. Skipping Episode 2, didn't really like that episode. (Just a heads up)**

 _ **Next Time on Stargate: Atlantis:**_ _ **38 minutes:**_

 **Sheppard and Co will encounter an Iratus bug and Jess gets it attatched to her neck, then they're stuck in the Stargate. They have only 38 minutes to get unstuck and get the bug off Sheppard.**


End file.
